Introductory Biophysics (With CD)

Contents: 

Chapter 1: Building Blocks and Structure • Atoms and Ions • Subatomic Particles • Atomic Constituents of Life Ions • Molecules Essential for Life • Water • Proteins • Lipids • Carbohydrates • Cholesterol • Nucleic Acid • What Is Life? • Requirements for Life  • Domains of Life • Characteristics of Living Cells • Structure of Living Cells  • Boundary of Life

Chapter 2: Living State Interactions • Forces and Molecular Bonds • Ionic Bonds • Covalent Bonds • Hydrogen Bonds • Van der Waal Forces • Electric and Thermal Interactions • Electric Dipoles • Polarization and Induced Dipoles • Casimir Interactions • Domains of Physics in Biology • Exercises

Chapter 3: Heat Transfer in Biomaterials • Heat Transfer Mechanisms • Conduction • Convection • Radiation • The Heat Equation • Transient Heat Flow • Steady State Heat Flow • Joule Heating of Tissue • Exercises

Chapter 4: Living State Thermodynamics • Thermodynamic Equilibrium • First Law of Thermodynamics and Conservation of Energy • Entropy and the Second Law of Thermodynamics • Does Life Violate the Second Law? • Measures of Entropy? • Free Expansion of a Gas • Physics of Many Particle Systems • How Boltzmann Factors in Biology • Canonical Partition Function • Average Energy • Entropy and Free Energy • Heat Capacity • Two-State Systems • Continuous Energy Distribution • Composite Systems • DNA Stretching • Casimir Contribution to the Free Energy • Lipid Bilayer Tubes • Rouleax • Protein Folding and Unfolding • Protein Unfolding • Levinthal's Paradox • Energy Landscape • Folding on a Lattice • Monte Carlo Methods • Folding @ home • Exercises

Chapter 5: Open Systems and Chemical Thermodynamics • Enthalpy, Gibbs Free Energy, and Chemical Potential • Chemical Reactions • First-Order Reactions • Second-Order Reactions • Activation Energy and Rate Constants • Detailed Balance • Nitrogen Fixation • Enzymatic Reactions • ATP Hydrolysis and Synthesis • Entropy of Mixing • The Grand Canonical Ensemble • Hemoglobin • Exercises

Chapter 6: Diffusion and Transport • Maxwell-Boltzmann Statistics • Brownian Motion • Fick's Laws of Diffusion • Fick's First Law • Fick's Second Law • Quantum Diffusion • Time-Independent Concentrations • Fick's Law for Growing Bacterial Cultures • Sedimentation of Cell Cultures • Diffusion in a Centrifuge • Diffusion in an Electric Field • Lateral Diffusion in Membranes • Navier-Stokes Equation • Reynolds Number • Low Reynolds Number Transport • Purcell's ?Life at Low Reynolds Number? • Coasting Distance of a Bacterium • Active and Passive Membrane Transport • Exercises

Chapter 7: Fluids • Laminar and Turbulent Fluid Flow • Bernoulli's Equation • Equation of Continuity • Venturi Effect • Fluid Dynamics of Circulatory Systems • Viscous Flow • Vessel Constriction and Aneurysm • Variation of Blood Pressure with Depth • Microgravity Effects • Capillary Action • Exercises

Chapter 8: Bioenergetics and Molecular Motors • Kinesins, Dyneins, and Microtubule Dynamics • Brownian Motors • Feynman Ratchet • Kinesin Brownian Dynamics • Myosin Brownian Dynamics • ATP Synthesis in Mitochondria • Electron Transport Chain • ATP Synthase • Torque Generation in ATP Synthase  • Photosynthesis in Chloroplasts • Photosystem II • Photosystem I • Light Absorption in Biomolecules • Vibrational Spectra of Biomolecules • Square Well Potential • Harmonic Oscillator Potential • Exercises

Chapter 9: Passive Electrical Properties of Living Cells • Poisson-Boltzmann Equation • One-One Valent Electrolytes • Low Field Limit • Spherical Solution • Intrinsic Membrane Potentials  • Induced Membrane Potentials • Plasma Membrane • Liposome in a Static Electric Field • Spherical Cell in an Alternating Electric Field • Inertial Effects in Field-Induced Counterion Motion • Induced Potentials in Organelle Membranes • Mitochondrion in an Alternating Electric Field • Bioimpedance • Time Harmonic Current Flow • Dielectric Spectroscopy • Deybe Relaxation Model • Cole Equation • Maxwell-Wagner Effect • Skin Impedance • Electrode Polarization • Bioimpedance Simulator • Nonlinear Effects • Exercises

Chapter 10: Nerve Conduction • Nerve Impulses • Neurotransmitters and Synapses • Passive Transport in Dendrites • Active Transport and the Hodgkin-Huxley Equations • Simulation of Action Potential • Excitation Threshold • Neuronal Refactoriness • Repetitive Spiking • FitzHugh-Nagumo Model • Action Potentials in the Earthworm Nerve Fiber • Exercises

Chapter 11: Mechanical Properties of Biomaterials • Elastic Moduli • Young's Modulus • Shear Modulus • Poisson's Ratio • Electric Stresses in Biological Membranes • Mechanical Effects of Microgravity During Spaceflight  • Exercises

Chapter 12: Biomagnetism • Biomagnetic Field Sources • Current Dipole Model • Vector Potential Formulation • Nerve impulses • Magnetotactic Bacteria • SQUID Magnetometry • Josephson Effect • Flux-Locked Loop • Intrinsic Noise Factors  Extrinsic Noise Factors • Digital Filters • Magnetocardiography • Fetal Magnetocardiography • Magnetoencephalography • Exercises

Chapter 13: Nonlinearity and Chaos in Biological Systems • Chaotic Dynamics • Characteristics of Chaotic Dynamics • Sensitive Dependence on Initial Conditions • Phase Space • Phase Space Reconstruction • Poincare Sections • Lyapunov Exponents • Power Spectra • Population Growth in a Limited Environment  • Predator-Prey Models of Population Dynamics  • Discrete Logistic Equation • Period-Doubling Route to Chaos • Bifurcation Diagrams • Lyapunov Exponent of the Logistic Equation • Shannon Entropy • Chaos in the Heart • Reaction Diffusion Equations • Action Potentials • Fertilization Calcium Waves • Pattern Formation • Dynamics of the Driven Hodgkin-Huxley System • Models of DNA Motility • Exercises

Chapter 14: Fractals and Complexity in the Life Sciences • Fractal Geometry • Computing Fractal Dimension • Fractal Structures in Biology • Fractal Ferns • Diffusion-Limited Aggregation • Power Laws in Biology • Self-Organized Criticality • BTW Sandpile Model • Extinction in the Bak-Sneppen Model  • Power Law Behavior in Chemical Reactions  • The Game of Life • SOC in the Game of Life • Exercises

Chapter 15: Life and the Universe • Astrobiology • Extremophiles • Primordial Soup, Interstellar Gas, and Dust • The Miller Experiment • Chemistry of the Interstellar Medium • Searches for Life in the Solar System • Mars • Europa • Lake Vostok • Search for Life Outside the Solar System • Extrasolar Planets • SET! Initiatives • Anticoded Signals • Frequency Domain Searches • Radio Interferometry • The Drake Equation • Implications for Life in the Multiverse Picture • The Multiverse • The Anthropic Principle • Multiverse Cosmological Models • Exercises

Appendix 1: Mathematical Formulas • Appendix 2: Overview of MATLAB@ • Appendix 3: Derivation of the Heat Equation • Appendix 4: Derivation of Shannon's Entropy Formula • Appendix 5: Thermodynamic Identities • Appendix 6: Kramers-Kronig Transformations • Appendix 7: Solution to the One-Dimensional Schrodinger Equation • Appendix 8: Biophysical Applications of QuickField??? • Appendix 9: Biological Material Properties • Appendix 10: Solutions of the Linearized Poisson-Boltzmann Equation • References and Further Reading • Index

About the Author: 

J. R. Claycomb (Ph.D) is currently an assistant professor in physics at Houston Baptist University. He teaches modern physics, biophysics and astronomy and his research interests include biophysics and magnetic measurements. He has published over 40 journal articles and is a consultant for various engineering companies.

Jonathan Quoc P. Tran has published journal articles in IEEE Transactions on Applied Superconductivity and The Physics Teacher. He graduated from Houston Baptist University in December 2008 with a degree in Biology, Biochemistry and Molecular Biology and currently studies medicine at the University of Texas Southwestern Medical Center.